Or you could just pick the combat oriented guardian stone so it's less annoying.
I mean, if I were to choose a spellsword type class, should I be annoyed that the first 3 stones don't cater to every skill I want to level?
But then most of your other skills would level less quickly. With a spellsword it's a little different because you would most likely have a pretty even split between combat and magic skills, meaning you just have to make a decision in regards to which type you want to give the increase to. But you would expect a pure thief to have as much of a purity advantage as a pure mage or warrior.
Once again, I'm saying this is only a small problem and will be completely not-existent once people have familiarised themselves with the locations of the stones, unless of course they RP someone who doesn't know the environment or whatever, but let's not get into all that.
Edit: Also, what's the bet that there is a battlemage-esque guardian stone? Pretty good chance.